Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

(no subject)
by Arvind Gururajan 09 Jun '05

09 Jun '05

Hello, I am very new to Freesurfer. Could anybody please tell me which specific MNI tool, I need to install? > > I tried the following command. > > ./recon-all -smooth1 ZM > ######################################## > program versions used > $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ > mri_convert --version > $ > strings: rawtominc:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > strings: minctracc:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > strings: mincresample:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > strings: mincaverage:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > mri_convert --version > $ > strings: mritotal:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > strings: nu_correct:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > ####################################### > ERROR: Flag ZM unrecognized. > -smooth1 ZM > > > The folder ZM has only one orig file in the surf directory. There are no > raw data(.COR files). Please let me know your feedback. > > Sincerely, > > Arvind Gururajan

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can left and right surfaces be flipped?
by peggy christidis 09 Jun '05

09 Jun '05

Hi there, I just finished creating a surface (with lots of time consuming manual editing) for someone who just informed me that he got the right-left orientation wrong on the volume I was given, and that it needs to be reversed (grrrrr....) Is there any way to do this in FreeSurfer without having to redo the surfaces? Thanks again, Peggy

4 6

control points and monkey brain
by peggy christidis 09 Jun '05

09 Jun '05

Hey everyone, Someone has given me a monkey volume (it's actually the average of 4 volumes and the gray-white matter contrast is pretty good) and I need to make a surface from it. I've never dealt with non-human datasets, but I did read in the freesurfer mailing archives that control points must always be added to a monkey T1 volume in order to get a decent wm segmentation. I ran recon-all stage1 and I got a first pass surface, and indeed I need to add control points because there is alot of white matter in the frontal lobes that is not being included in the segmentation. So I selected some control points (in the T1 volume, within the white matter), and then I ran this command: recon-all stage1 -usecontrolpoints -subjid monkey_surf I looked at the output and it doesn't seem to have helped at all. The segmentation still doesn't include the wm where the control points were added. What am I doing wrong? I've attached a jpg file to illustrate my problem. Thanks, Peggy

2 1

TIV and associated label
by Elizabeth Fenstermacher 09 Jun '05

09 Jun '05

Hello All, I was hoping to add a column for TIV in the calc_vols script I've been using to calculate the volumes of various ROIs. Is there an associated label for the TIV or is that something that would need to be created? Thanks! Eliz

1 0

Inflate from original surface files
by Arvind Gururajan 09 Jun '05

09 Jun '05

Hello, We have already generated a number of original surface files (.orig) in our lab. We were wondering if there is a way to generate the smooth and the inflated surface from the existing .orig files? Could you provide us a seperate tool to do this conversion? Sincerely, Arvind Gururajan

2 1

RE: [Freesurfer] recon-all-nmr -disable-autoseg
by Fornito, Alexander 08 Jun '05

08 Jun '05

I can't find any usage or help for parcellate_subject, and if I simply run parcellate_subject [subjname], I get the following message: CSURF_DIR: Undefined variable. Any clues? Thanks, A. -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 6/9/2005 1:10 AM To: Bruce Fischl Cc: Fornito, Alexander; Elizabeth Fenstermacher; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg I think it looks in the average7 directory for a few labels (central sulc, calc, ...), then maps them to your subject through the registration. The intent was that you could then look at these labels to make sure they were in about the right place. doug Bruce Fischl wrote: > the labels are deprecated since we have the cortical parcellation. And > yes, run parcellate_subject and it will create *.annot files in the > label dir. > cheers, > Bruce > > On Wed, 8 Jun 2005, Fornito, Alexander wrote: > >> That worked, thanks, Doug. >> To expand on the labels issue, from my understanding, the labels are >> used to check that the registration worked, and that these are >> automatically created. >> I don't have any files in my labels directory. >> Do you need to run parcellate_subject to get them? >> Is there any documentation on parcellate_subject? I tried to run it >> and got the message: >> CSURF_DIR: Undefined variable. >> >> as an aside, where is the average7 surface. I though it might be in >> /usr/local/freesurfer/average/, but I don't seem to be able to open >> any of the files in there with tksurfer. >> Thanks again, >> Alex >> >> >> >> -----Original Message----- >> From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Wed 6/8/2005 11:08 AM >> To: Elizabeth Fenstermacher >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg >> use the one in dev not std env >> >> >> Elizabeth Fenstermacher wrote: >> >>> >>> Hello All, >>> >>> I have a number of jobs that I will be running through recon-all-nmr >>> -stage1 in the next few days. I tried using the -disable-autoseg >>> flag, but it seems not to work as the jobs I submitted this morning >>> have now run for 50 minutes. >>> >>> The command line as I typed it was >>> >>> pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor >>> -usenuintensitycor -disable-autoseg" >>> >>> perhaps I've misplaced the flag? If anyone has any insight as to why >>> it seems to be persitting in running the autoseg I would appreciate it. >>> >>> Thanks! >>> Eliz >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

freesurfer course
by Kerr, Catherine E. 08 Jun '05

08 Jun '05

Someone told me there was going to be a freesurfer course at the NMR center in July. Is it possible to register? Who would have this information? Thanks

2 1

RE: [Freesurfer] recon-all-nmr -disable-autoseg
by Fornito, Alexander 08 Jun '05

08 Jun '05

That worked, thanks, Doug. To expand on the labels issue, from my understanding, the labels are used to check that the registration worked, and that these are automatically created. I don't have any files in my labels directory. Do you need to run parcellate_subject to get them? Is there any documentation on parcellate_subject? I tried to run it and got the message: CSURF_DIR: Undefined variable. as an aside, where is the average7 surface. I though it might be in /usr/local/freesurfer/average/, but I don't seem to be able to open any of the files in there with tksurfer. Thanks again, Alex -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wed 6/8/2005 11:08 AM To: Elizabeth Fenstermacher Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg use the one in dev not std env Elizabeth Fenstermacher wrote: > > Hello All, > > I have a number of jobs that I will be running through recon-all-nmr > -stage1 in the next few days. I tried using the -disable-autoseg > flag, but it seems not to work as the jobs I submitted this morning > have now run for 50 minutes. > > The command line as I typed it was > > pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor > -usenuintensitycor -disable-autoseg" > > perhaps I've misplaced the flag? If anyone has any insight as to why > it seems to be persitting in running the autoseg I would appreciate it. > > Thanks! > Eliz > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

recon-all-nmr -disable-autoseg
by Elizabeth Fenstermacher 07 Jun '05

07 Jun '05

Hello All, I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not to work as the jobs I submitted this morning have now run for 50 minutes. The command line as I typed it was pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor -usenuintensitycor -disable-autoseg" perhaps I've misplaced the flag? If anyone has any insight as to why it seems to be persitting in running the autoseg I would appreciate it. Thanks! Eliz

4 3

recon-all stage4b error
by Fornito, Alexander 07 Jun '05

07 Jun '05

Hi all, I've created my the fional surface for some people and am trying to register them using recon-all -stage4b.However, I get an error message saying that I needed to do average labels (see output below). I've noticed that I get the same message if I try to morph_subject, except morph_subject actually creates sphere.reg files. Am I missing something? Thanks for your patience! Alex recon-all -subjid 186 -stage4b ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects ERROR: cannot subject average7, needed to do average labels.

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Freesurfer